CCS-33 SP-587 : Add display of parent and intervals to the strain browser.

SVN: 29172

eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/basynthec-browser.js

@@ -411,7 +411,7 @@ AppPresenter.prototype.retrieveOd600DataForDataSet = function(ds)
 	var tsvPathInDataSet = "";
 	ds.files.forEach(function (file) { if (endsWith(file.pathInDataSet, "xls.tsv")) tsvPathInDataSet = file.pathInDataSet});
 		
-	var tsvUrl = dssUrl + "/" + ds.bis.code + "/" + tsvPathInDataSet + "?sessionID=" + basynthec.server.getSession();
+	var tsvUrl = dssUrl + "/" + ds.bis.code + "/" + tsvPathInDataSet + "?sessionID=" + basynthec.server.sessionToken;
 	
 	var lexicalParent = this;
 
@@ -1040,6 +1040,8 @@ Od600InspectorView.prototype.updateView = function(duration)
 		});
 
 	appendGrowthSection(inspectorEnter);
+	appendParentSection(inspectorEnter);
+	appendIntervalsSection(inspectorEnter);
 	
 	appendObjectSection({
 		getSectionContainer: function(){
@@ -1182,6 +1184,32 @@ Od600InspectorView.prototype.updateView = function(duration)
 		.remove();
 }
 
+function appendParentSection(inspectorEnter) {
+	var parentSection = inspectorEnter.append("div");
+	var parents = parentSection.selectAll("div.parent")
+		.data(function(d) { return [d.data.parent]; });
+	parents.enter().append("div")
+		.attr("class", "parent")
+		.text("Parent: ");
+	parents.selectAll("span")
+		.data(function(d) { return [d] })
+	.enter().append("span")
+		.text(function (d) { return (d) ? d : "None" });
+}
+
+function appendIntervalsSection(inspectorEnter) {
+	var intervalsSection = inspectorEnter.append("div");
+	var intervals = intervalsSection.selectAll("div.intervals")
+		.data(function(d) {	return [d.data.intervals]; });
+	intervals.enter().append("div")
+		.attr("class", "intervals")
+		.text("Intervals: ");
+	intervals.selectAll("span")
+		.data(function(d) { return d; })
+	.enter().append("span")
+		.text(function (d) { return d + " " });
+}
+
 function appendGrowthSection(inspectorEnter) {
 	var growthMediaSection = inspectorEnter.append("div");
 	var growsSection = growthMediaSection.selectAll("div.growth")

eu_basynthec/source/core-plugins/basynthec/1/as/webapps/basynthec/browser/openbis-basynthec.js

@@ -64,7 +64,7 @@ openbis_basynthec.prototype.getStrains = function(dataSet)
 
 openbis_basynthec.prototype.getStrainsPhenotypesAndPredictions = function(action){
 	this.server.createReportFromAggregationService("DSS1","chicago", null, function(response){
-		var result = [];
+		var result = {};
 		
 		if(response.result && response.result.rows){
 			$.each(response.result.rows, function(index, row){
@@ -72,6 +72,8 @@ openbis_basynthec.prototype.getStrainsPhenotypesAndPredictions = function(action
 				strain.name = strain.id;
 				strain.hasPredictions = strain.predictions != null && strain.predictions.length > 0;
 				strain.hasPhenotypes = strain.phenotypes != null && strain.phenotypes.length > 0;
+				strain.hasParent = strain.parent != null;
+				strain.hasIntervals = strain.intervals != null;
 				result[strain.id] = strain;
 			});
 		}

eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-file-and-put-to-table.py

@@ -29,7 +29,7 @@ def indexDataByStrainId(data):
   dataById = {}
   for strainData in data:
     tokens = strainData.strip("{}  \n").split(',')
-    theIds = [token for token in tokens if token.startswith('"id"')]
+    theIds = [token for token in tokens if token.strip().startswith('"id"')]
     if (len(theIds) < 1):
        continue
     theId = theIds[0].split(':')[1].strip('"  \n')
@@ -65,7 +65,6 @@ def filterToUnknownStrains(dataSets, dataById):
     for strain in strains:
       if dataById.get(strain) is None:
         unknownStrains.add(strain)
-  print unknownStrains
   return unknownStrains
 
 def aggregate(parameters, table):

eu_basynthec/source/core-plugins/basynthec/1/dss/reporting-plugins/chicago/load-data-from-server-and-save-in-file.py

@@ -8,11 +8,19 @@ import shutil
 FIELD_ID = 'id'
 FIELD_PREDICTIONS = 'predictions'
 FIELD_PHENOTYPES = 'phenotypes'
+FIELD_PARENT = 'parent'
+FIELD_INTERVALS = 'intervals'
 
 def loadDataFromServer(serverUrl):
   url = urllib.urlopen(serverUrl)
   return url.read().decode('utf8')
 
+def loadDataFromFile(filePath):
+  dataFile = open(filePath, 'r')
+  data = file.read(dataFile)
+  dataFile.close()
+  return data
+
 def convertData(dataString):
   jsonList = json.loads(dataString)
   dataList = []
@@ -21,7 +29,9 @@ def convertData(dataString):
     id = jsonItem[FIELD_ID].upper() 
     predictions = jsonItem[FIELD_PREDICTIONS]
     phenotypes = jsonItem[FIELD_PHENOTYPES]
-    dataList.append({FIELD_ID: id, FIELD_PREDICTIONS: predictions, FIELD_PHENOTYPES: phenotypes})
+    parent = jsonItem[FIELD_PARENT]
+    intervals = jsonItem[FIELD_INTERVALS]
+    dataList.append({FIELD_ID: id, FIELD_PREDICTIONS: predictions, FIELD_PHENOTYPES: phenotypes, FIELD_PARENT: parent, FIELD_INTERVALS: intervals})
 
   return dataList
 
@@ -42,6 +52,7 @@ def writeDataToFile(filePath, dataList):
       file.close()
 
 data = loadDataFromServer('http://pubseed.theseed.org/model-prod/StrainServer.cgi?user=reviewer&pass=reviewer&method=getAllPhenotypesAndPredictions&encoding=json')
+#data = loadDataFromFile('original-data-from-server.json')
 writeDataToFile('data-from-server.csv.tmp', convertData(data))
 shutil.move('data-from-server.csv.tmp', 'data-from-server.csv')